A Year Without Germs

Months of exuberant hand-sanitizing and social isolation during the pandemic have changed our exposure to microbes, in ways good and bad.

A patterned silhouette of a human body, with shimmering dots
Adam Maida / The Atlantic

Sales of alcohol surged in 2020, especially among the higher-proof varieties. But one type far outsold the others: hand sanitizer.

In the heat of the pandemic, Purell poured some $400 million into expanding its production. As anyone who resorted to bootleg hand sanitizer knows, the company came nowhere close to meeting demand. Distilleries and state governments also got in on the action; New York State’s version was, as best as I could discern, a mixture of urinal cakes and bottom-shelf vodka. (I was grateful for it.) All told, by the end of 2020, sales of hand sanitizer had increased by 600 percent.

Some of this sanitizer is presumably still sitting untouched in people’s pandemic pantry stockpiles. But much of it also went onto our skin, where the alcohol hastily dissolves most of the viruses, bacteria, and fungi it encounters. This dramatic increase in personal sterilization—combined with many other microbe-reducing habits, including masking and physical distancing—have prompted some biologists to wonder, in academic papers and prominent op-eds, about the extent of the “collateral damage” to our immune system.

To get this out of the way: Destroying the coronavirus is, without question, paramount. Millions of people are dead, and tens of thousands more die every week. At the same time, the majority of the trillions of microbes that inhabit our skin and gut—collectively, our microbiome—are either harmless or helpful. “The microbes we carry around are involved in many of the fundamental processes of Homo sapiens,” Brett Finlay, a professor of microbiology and immunology at the University of British Columbia, in Canada, told me. Among their other roles, these organisms interact with the immune cells in our skin and teach them to respond only to serious threats. The overall effect of messing with our microbes is not manifestly good or bad, but it is also manifestly not zero.

Our microbiome is constantly in low-level flux, depending on our environment—the people around us, the food we eat, the soaps we use, and so on. But many of our environments and daily routines have changed dramatically over the past year as a result of the extreme focus on hygiene and potential viral exposures of all sorts. This has almost certainly had substantive effects on our microbiome diversity, individually and collectively, Finlay said. “The concern among some microbiologists, for the last decade or so, has been that the collateral damage of excessive sanitizing and use of antibiotics is not good, in terms of microbes that we spent thousands of years evolving with.” He cited links between antibiotic overuse and increasing rates of asthma and obesity, as well as a smattering of evidence about the beneficial effects of vaginal deliveries versus Cesarean sections. There is also evidence that having a diverse microbiome is an indicator—if not necessarily a driver—of good health.

The pandemic may have accelerated that loss of diversity. In recent weeks, Finlay has been quoted on the subject in several news stories, as concerned work-from-homers begin to reckon with the long-term effects of their extended isolation. “When COVID hit, it created a fantastic experiment that’s ongoing,” Finlay told me. “We have completely changed our behaviors, and when you do that, you change your microbial exposures: You’re not hugging and kissing people, not riding the subways; you’re spending more time at home making bread.” (How did he know?)

It’s too early to be certain of the effects, Finlay said, and any correlations could take decades to bear out. But he’s especially concerned about the very young and the very old, whose microbiomes are most labile. They also happen to be the groups whose daily lives were most affected by the pandemic. “Kids haven’t been in day care or preschool,” Finlay said. “Elderly people have been isolated from their grandkids, who usually slobber all over them.”

He is far from alone in this line of worry. “As a parent—not just as a researcher—I was extremely concerned by a lot of the plans for intense sanitizing in schools,” Melissa Melby, a medical anthropologist at the University of Delaware, told me. “The number of people reporting they were sanitizing everything they brought into their houses was pretty tremendous, and I think we have good reason to believe that dramatic changes in hygiene and sanitizing behaviors will affect our microbes, particularly for young children.”

One result of this has already been observed: We’ve broken chains of transmission for all sorts of disease-causing pathogens, including common-cold viruses and influenza. Cases of these illnesses last winter were at recent-historic lows. And now that I think of it, it’s been more than a year since I’ve had a cold. I used to get them all the time, even though I’m pretty careful. Microbiome experts are not suggesting that it’s good to get lots of common colds; they say we should be grateful for the recent dip in these infections, just as we’re grateful that we haven’t lately stepped on a rusty nail. The “what doesn’t kill you” adage does not apply to respiratory infections any more than it does to tetanus.

The more interesting question is whether I might have missed out on contact with other, more useful microbes along the way. I can’t remember the last time I shook someone’s hand. Whenever it was, it might have been the last time ever.

A recent piece in The New York Times described researchers’ “mounting sense of dread” about these behavioral changes and their potentially “irreversible consequences.” But some are feeling optimistic. Certain effects could be positive, says Martin Blaser, the director of the Center for Advanced Biotechnology and Medicine at Rutgers University. For one thing, because people didn’t get colds, they also didn’t get (inappropriately) prescribed antibiotics. Many of these are crucial, even lifesaving, therapies. Used too often, though, they can disrupt microbial diversity in the body. If the pandemic helped mitigate their overuse and misuse, that’s “unquestionably good” from Blaser’s point of view.

As for those of us whose microbiome might be lacking because of isolation, Blaser has more hope. “The microbiome in older kids and adults is very resilient,” he says. The microbes that we acquire from other people later in life don’t seem to stick around so long, or to fundamentally alter the microbial foundation that each person develops very early in life. Married couples, for instance, share far less of their biomes than do a mother and child.

Whether the loss of social contact over the past year matters for our microbes in the long term depends on how we transition out of this period. For older kids and most adults, Finlay reassured me, “the damage is not irreversible.” That is, your microbial diversity may fall, but your foundation stays with you. High-fiber diets can help bring the diversity up again. “Instead of a sugar and white-flour diet, try to eat more nuts and seeds and legumes,” Finlay recommended. Spend time outside when you can, and hang out with animals. “Dogs are a great way to get microbial exposure.”

For me, this was all very reassuring. I got a dog during the pandemic, and I’ve spent a lot of time outdoors because there’s been nothing else to do. I’ve also eaten better because I’m cooking more and not grabbing a pizza slice every few hours (this is what New Yorkers do). You know, this pandemic may have been okay for my microbes. Maybe even good?

It’s not just me. In many families, young children were able to spend more time with their parents and pets than they otherwise would have. “I actually got my family outdoors more,” Melby, the medical anthropologist, told me. But these benefits have not been uniform across the population. Although “some people have improved their lives in terms of microbial exposure,” she said, “I know a lot of people who went the other direction.” Among the latter are those who have lacked access to safe parks and neighborhoods, high-quality food, and clean air. “I think the way this is going to play out is going to be very dependent on what resources people had during the pandemic.”

“If they have the income to do it, there are measures people can take to make sure their young children develop a healthy microbiome,” says Tamara Giles-Vernick, who studies medical ethnohistory at Institut Pasteur. In particular, she says, breastfeeding at an early age seems to play a role in setting the foundation of a child’s microbiome. This may have been easier during the pandemic than during normal times, for people who have worked from home. For those who have had to take on second jobs, the inverse is true.

A microbiome gap is evident even in nonpandemic times. “Generally, communities of lower socioeconomic status tend to have less diverse microbiomes,” says Katherine Amato, a biological anthropologist at Northwestern University. In its most extreme form, this paucity is known as “dysbiosis” and is strongly associated with metabolic and autoimmune disorders. But the research is just beginning to scratch the surface in terms of microbial disparities, Amato says. “Things like stress, diet, shift work, and disturbances in circadian rhythms can have negative impacts on the microbiome.” Baseline inequities that affect the microbiome are clearly playing into the disparities in who’s dying of COVID-19. Whether the microbiome itself is a factor in those outcomes remains to be seen.

“Many high-income countries have moved to vaccinate the elderly first, and that’s incredibly important in terms of reestablishing normal microbial inputs,” Giles-Vernick says. Opening up nursing homes to outside visitors as soon as possible, too, may have more than purely social and psychological benefits. The same goes for common areas in nature. “In France, we’re in confinement, but unlike last spring, we can go to parks,” Giles-Vernick says. “That’s a really important measure.”

The ongoing challenge is to avoid binary thinking about microbes: They are not simply good or bad, any more than people are, and neither is Purell. “Everything can be overdone,” Blaser reminds me, and that includes sterilizing things. We should instead make targeted hygiene the goal—and focus on the proven, effective methods to prevent disease transmission. Hand sanitizer can be a miracle during a cholera outbreak; that doesn’t mean you should shower in it after every Zoom call.

(If you do this, contact one of these researchers.)